deposit

An R6 client for getting virion data and metadata.

Value

A deposit class (R6 class)

invisibly returns self

dataframe of remote csv file.

String. Path to download location.

data.frame from readr::read_csv()

String. cleaned zenodo id

metadata in the specificed format (invisible)

List. Named list of data frames with the following fields:

name = field name
type = field type
description = characterization of the field

parent_id String. Identifier for a Zenodo deposit with multiple versions.

all_versions Character. All zenodo ids for versions of the deposit.

summary_df Data frame. A table of all zenodo ids for versions of the deposit.

latest_version String. Identifier for the latest version of the zenodo deposit.

working_version String. Identifier for the version of the zenodo deposit you are working with

working_bibtex String. Bibtex for the version of the zenodo deposit you are working with.

working_citation String. Citation for the version of the zenodo deposit you are working with.

working_files Data frame. Working files consist of key (file name) and url (url to file on zenodo)

working_json list. Metadata for the working version.

Methods

Public methods

deposit$new()
deposit$set_working_version()
deposit$load_remote_csv_file()
deposit$download_versioned_data()
deposit$load_local_csv_file()
deposit$check_zenodo_id()
deposit$export_metadata()
deposit$get_data_dictionary()
deposit$get_parent_id()
deposit$get_all_versions()
deposit$get_summary_df()
deposit$get_latest_version()
deposit$get_working_version()
deposit$get_working_bibtex()
deposit$get_working_citation()
deposit$get_working_files()
deposit$get_working_json()
deposit$clone()

Method `new()`

Create a new deposit object, as an R6 client. This object is connected to the zenodo deposit for virion and is the gateway for accessing different versions of the data.

Usage

deposit$new(parent_id = "15643003")

Arguments

parent_id: String. Identifier for a Zenodo deposit with multiple versions.

Returns

A new deposit object

Examples

\dontrun{
virion_deposit <- deposit$new()
}

Method `set_working_version()`

Set the version of the data you would like to work with. Note that the structure of Virion data may change through time.

Usage

deposit$set_working_version(
  zenodo_id = "latest",
  style = "apa",
  print_bibtex = TRUE,
  print_citation = TRUE
)

Arguments

zenodo_id: String. A zenodo id or latest.
style: String. The citation style to be used.
print_bibtex: Logical. Should the bibtex for the working version of the deposit be printed when setting the working version?
print_citation: Logical. Should the citation for the working version of the deposit be printed?

Examples


\dontrun{
# set the working version to the latest version of the deposit
virion_deposit$set_working_version("latest")

# set the working versino to an arbitrary deposit
virion_deposit$get_all_versions()
virion_deposit$set_working_version("19502921")
}

Method `load_remote_csv_file()`

Load a remote csv listed in the working files field directly into the environment.

Can handle either csv or csv.gz files. This function downloads a temporary file to your machine, reads it, then returns a dataframe.

The local file cache is removed when your R session restarts.

Consider using the download_versioned_data to save a persistent version of the virion dataset on your machine.

Usage

deposit$load_remote_csv_file(file_key, refresh = FALSE, ...)

Arguments

file_key: String. A file key as seen in the working_files field
refresh: Logical. Should files be re-downloaded.
...: Additional arguments to pass to readr::read_csv()

Examples

\dontrun{
## see the working files
working_files <- virion$get_working_files()
working_files$file_key
virion_data <- virion_deposit$load_remote_csv_file("virion.csv.gz")

}

Method `download_versioned_data()`

Download versioned data

Downloads all the files for a particular version of Virion to dir/zenodo_id.

This function does not change the working version!

Usage

deposit$download_versioned_data(
  zenodo_id = "working",
  dir = "outputs",
  refresh = FALSE
)

Arguments

zenodo_id: String. A zenodo id, working or latest
dir: String. Storage location for files
refresh: Logical. Should files be re-downloaded.

Examples

\dontrun{
# download files for the working version
virion_deposit$download_versioned_data()

# download files for the latest version
virion_deposit$download_versioned_data("latest")

# download files for some zenodo id
virion_deposit$download_versioned_data("19502921")
}

Method `load_local_csv_file()`

Load a local version of the csv.

Assumes you would like to load the file from the current working version.

If the csv file is not present, a persistent version of the file will be downloaded to your machine.

Usage

deposit$load_local_csv_file(file_key, refresh, ...)

Arguments

file_key: string. Name of file from working_files
refresh: logical. Should the file be re-downloaded?
...: Additional parameters to pass to readr::read_csv()

Examples

\dontrun{

virion <- deposit$new()
virion$set_working_version()
working_files <- virion$get_working_files()
working_files$file_key
virion$load_local_csv_file("virion.csv.gz")
}

Method `check_zenodo_id()`

Check the zenodo ID

Look for key words like working or latest and convert them to integer ids OR pass the zenodo id directly to sanitize_id()

Usage

deposit$check_zenodo_id(zenodo_id)

Arguments

zenodo_id: String. One of working, latest, or a zenodo id

Examples


\dontrun{
virion_deposit$check_zenodo_id("latest")
}

Method `export_metadata()`

Export metadata for a version of the deposit.

Usage

deposit$export_metadata(zenodo_id, format, verbose)

Arguments

zenodo_id: String. One of "latest","working", or a zenodo id
format: String. One of "json", "json-ld","csl","datacite-json","datacite-xml", "dublincore","marcxml","bibtex","geojson","dcat-ap","codemeta", "cff"
verbose: Logical. Print the metadata

Examples


\dontrun{
 virion_deposit$export_metadata("working")
}

Method `get_data_dictionary()`

Create a list of data dictionaries.

Usage

deposit$get_data_dictionary(
  file_key = "datapackage.json",
  dir = tempdir(),
  refresh
)

Arguments

file_key: string. Name of file from working_files
dir: string. Name of directory
refresh: refresh Logical. Should files be re-downloaded.